[gmx-users] simulation of a dimer

[Mark Abraham]

priya priya wrote:
> Dear All
> I am trying to simulate a dimer in water, wheneever i run a energy 
> minimization on it there ia a peptide bond created between the two 
> chains. i have tried to include the pdb  of one chain in the other and 
> then started off but again same results.

This is not possible. I guess that this peptide bond is "created" by 
pdb2gmx and you haven't seen it in your topology. I suggest you read 
"man pdb2gmx" to find out how to control its management of multi-chain 
pdb files and then construct a pdb file with the two molecules in 
different chains.

Mark